Box of Archives
The "Box of Archives" section on the WEHI-ResearchComputing's Imaging Getting Started Wiki showcases a curated collection of historical documents and software tools. It highlights the contributions of previous intern teams, documenting their development of a custom computational platform. This archive offers valuable insights into the evolution of imaging science, serving as an educational resource for new researchers in the field.
- This page contains documentation for the custom platform:
- The custom platform submits jobs to Galaxy.
- About Galaxy
Galaxy is an open-source, web-based platform that provides a user-friendly environment for performing data analysis, particularly in the fields of bioinformatics and computational biology. It was developed to make complex computational tools and workflows more accessible to researchers who may not have extensive programming experience.
Key features of Galaxy include:
- Web-based Interface: Galaxy is accessible through a web browser, eliminating the need for complex installations on individual computers. This feature allows users to access the platform from anywhere with an internet connection.
- Reproducible Workflows: Galaxy allows users to create and share workflows, which are sequences of computational steps. These workflows can be saved, shared, and reused by other researchers, ensuring the reproducibility of data analysis.
- Tool Integration: Galaxy provides a wide range of computational tools and algorithms for various bioinformatics tasks, such as sequence analysis, genome assembly, protein structure prediction, and more. These tools are integrated into the platform and can be combined to create custom analysis workflows.
- Data Management: Galaxy includes features for uploading, organizing, and managing data within the platform. This ensures that data used in analyses is readily available and can be easily shared with collaborators.
- Collaboration: Galaxy allows multiple users to work on the same project simultaneously, facilitating collaboration and enabling researchers to share their analysis processes and results with others.
- Visualization: Galaxy provides interactive visualizations and charts to help users interpret and analyze their data effectively.
First, Install Galaxy. Follow this tutorial to tart using Galaxy for image analysis. Visit Galaxy Documentation as you need.
Pros:
- User-Friendly Interface: Galaxy provides a web-based GUI with drag-and-drop functionality, making it accessible to researchers without programming experience.
- Extensive Toolset: Galaxy offers a wide range of pre-built tools for bioinformatics analyses, making it convenient for users to perform common tasks.
- Collaboration and Sharing: Galaxy facilitates sharing of workflows and datasets among users, promoting collaboration and enabling reproducibility.
- Managed Execution: Workflows are executed on Galaxy servers, reducing the need for users to manage computing resources.
Cons:
- Limited Flexibility: Galaxy's GUI-driven approach may be limiting for users who require more advanced customization and optimization in their workflows.
- Dependent on Galaxy's Ecosystem: Users are tied to Galaxy's toolset and may encounter limitations when using tools not available in Galaxy's environment.
- Server Resource Limitations: Public Galaxy servers may have restrictions on data storage and execution time.
Napari-lattice is a Python plugin that offers functionality for deskewing, cropping, visualization, and the creation of custom analysis pipelines specifically tailored for lattice lightsheet data, particularly from the Zeiss Lattice Lightsheet system. This plugin has been optimized to operate efficiently in headless mode.
Here is a comparison table organised by previous students:
